Sébastien Gagneux, Associate Professor, PhD

Function(s)
Head of Department

Qualification
Associate Professor of Infection Biology

Sébastien Gagneux is Associate Professor of Infection Biology and Head of the Department of Medical Parasitology and Infection Biology at the Swiss Tropical and Public Health Institute (Swiss TPH)/University of Basel. After receiving his PhD from the University of Basel, he worked as a postdoctoral fellow at Stanford University and at the Institute for Systems Biology in Seattle, USA. He then spent three years as a Program Leader at the MRC National Institute for Medical Research in London, UK before joining Swiss TPH. His research focuses on the ecology and evolution of Mycobacterium tuberculosis, and combines population genomics, molecular epidemiology and experimental approaches to study the effect of bacterial variation on host-pathogen interaction and drug resistance.

Research activities at Swiss TPH

  • Population genomics of Mycobacterium tuberculosis
  • Ecology and evolution of antibiotic resistance in Mycobacterium tuberculosis
  • Genomic epidemiology of tuberculosis

Higher education

  • MSc, 1997: Biology & Medical Parasitology, Swiss Tropical Institute/University of Basel, Switzerland
  • PhD, 2001: Epidemiology, Swiss Tropical Institute/University of Basel, Switzerland
  • 2001-2005: Postdoc, Division of Infectious Diseases & Geographic Medicine, Stanford University, USA
  • 2005-2006: Postdoc, Institute for Systems Biology, Seattle, USA

Work experience

  • 2016- : Associate Professor of Infection Biology, Swiss TPH/University of Basel, Basel, Switzerland
  • 2016- : Head of Department, Department of Medical Parasitology & Infection Biology, Swiss TPH, Basel, Switzerland
  • 2014-2016: Deputy Head of Department, Department of Medical Parasitology & Infection Biology, Swiss TPH, Basel, Switzerland
  • 2010-2016: SNF-Professor, Swiss TPH/University of Basel, Basel, Switzerland
  • 2007-2010: Programme Leader, Medical Research Council, National Institute for Medical Research, London, UK
  • 2006-2007: Senior Scientist, Institute for Systems Biology, Seattle, USA

Asare P et al. Whole genome sequencing and spatial analysis identifies recent tuberculosis transmission hotspots in Ghana. Front Med (Lausanne). 2020;7:161. DOI: 10.3389/fmed.2020.00161

Castro R.A.D et al. The genetic background modulates the evolution of fluoroquinolone-resistance in Mycobacterium tuberculosis. Mol Biol Evol. 2020;37(1):195-207. DOI: 10.1093/molbev/msz214

Ezewudo M et al. Author correction: Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. Sci Rep. 2020;10(1):3531. DOI: 10.1038/s41598-020-58955-y

Haraka F et al. Effect of history of tuberculosis on specificity of Xpert MTB/RIF. Eur Respir J. 2020(in press). DOI: 10.1183/13993003.00343-2020

Loiseau C et al. HIV coinfection is associated with low fitness rpoB variants in rifampicin-resistant Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2020(in press). DOI: 10.1128/AAC.00782-20

Loiseau C et al. An African origin for Mycobacterium bovis. Evol Med Public Health. 2020;2020:49-59. DOI: 10.1093/emph/eoaa005

McHenry M.L et al. Interaction between host genes and Mycobacterium tuberculosis lineage can affect tuberculosis severity: evidence for coevolution?. PLoS Genet. 2020;16(4):e1008728. DOI: 10.1371/journal.pgen.1008728

Menardo F, Gagneux S, Freund F. Multiple merger genealogies in outbreaks of Mycobacterium tuberculosis. Mol Biol Evol. 2020(in press). DOI: 10.1093/molbev/msaa179

Ngabonziza J.C.S et al. A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nat Commun. 2020;11:2917. DOI: 10.1038/s41467-020-16626-6

Oyas O et al. Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2020;117(15):8494-8502. DOI: 10.1073/pnas.1915551117